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James Holden is XO (Executive Officer) of an ice miner making runs from the rings of Saturn to the mining stations of the Belt. When he and his crew stumble upon a derelict ship, the Scopuli, they find themselves in possession of a secret they never wanted. A secret that someone is willing to kill for – and kill on a scale unfathomable to Jim and his crew. War is brewing in the system unless he can find out who left the ship and why.

Detective Miller is looking for a girl. One girl in a system of billions, but her parents have money and money talks. When the trail leads him to the Scopuli and rebel sympathizer Holden, he realizes that this girl may be the key to everything.

Humanity has colonized the planets - interstellar travel is still beyond our reach, but the Sol system has become a loose network of colonies. But there are tensions - the mineral-rich outer planets resent their dependence on Earth and Mars and the political and military clout they wield over the Belt and beyond.

Now, when Captain Jim Holden's ice miner stumbles across a derelict, abandoned ship, he uncovers a secret that threatens to throw the entire system into war. Attacked by a stealth ship thought to belong to the Mars fleet, Holden must find a way to uncover the motives behind the attack, stop a war and find the truth behind a vast conspiracy that threatens the entire human race.

Two hundred years after migrating into space, mankind is in turmoil. When a reluctant ship’s captain and washed-up detective find themselves involved in the case of a missing girl, what they discover brings our solar system to the brink of civil war, and exposes the greatest conspiracy in human history.[1]

Juliette Andromeda Mao has been abducted from her ship, the Scopuli, and left in a storage locker for 8 days. She breaks out only to find the crew gone and the ship's reactor shut down and covered by a flesh-like biologically active substance. The head of one of her crewmates pokes out from the accumulated biomass and asks her for help.

The Pure 'n' Kleen ice hauler Canterbury intercepts a distress signal from the Scopuli. An away team consisting of the ship's XO (Executive Officer) James Holden, engineers Naomi Nagata and Amos Burton, medical technician Shed Garvey, and pilot Alex Kamal intercept it on the shuttle Knight. They find the Scopuli powerless, with the distress signal emanating from a beacon with a Mars Congressional Republic Navy (MCRN) battery in it. The away team suspect pirates and head back to the Canterbury; however, the vessel is attacked and destroyed by a number of unidentified stealth ships before they make it back.

Holden, now captain of the Knight, broadcasts a message detailing the Cant's destruction, implicating the MCRN in the attack. Pure 'n' Kleen instructs them to meet up with the MCRN flagship, the Donnager, to assist with the investigation. While en route, Holden receives a message from Fred Johnson – the de facto leader of the Outer Planets Alliance (OPA), nicknamed the "butcher of Anderson Station" – on Tycho Station, declaring his support for the former, should the situation worsen. Six stealth ships begin following them.

On Ceres, the largest asteroid in the Asteroid Belt between Mars and Jupiter, Star Helix Detective Josephus Miller, a Belter born on Ceres, but working for the Earth security force there, is given a case to track down Julie Mao and send her back home to her parents on Luna. Riots break out after Holden's transmission about the Cant's destruction at the presumed hands of the MCRN, and it turns out all the station's riot gear is missing. With things getting harry, Miller's partner Havelock, an Earther, resigns and gets a new job working for Protogen Security.

On the Donnager, Holden is debriefed and Captain Yao insists that the MCRN had nothing to do with the Cant's destruction. The stealth ships attack; the Donnager is ultimately no match and the ship is boarded. Shed is killed when a gauss round (railgun) decapitates him. Since Holden and his crew are the only ones that can exculpate the MCRN, Yao orders Lt. Kelly to get them off the ship; they escape on the light frigate Tachi just before Yao self-destructs the Donnager.

Lt. Kelly, wounded during the escape, dies. Unsure of where to go next, Holden decides to take Fred Johnson up on his offer, so they head to Tycho Station. Fred gives them a new transponder code and Holden renames their ship the Rocinante.

While going through Julie's files, Detective Miller finds a message from Julie's parents warning her of an impending attack, sent two weeks before the Canterbury was destroyed. Anderson Dawes, leader of the Ceres branch of the OPA, tells Miller that Julie was on the Scopuli, and that Miller should lay off the Mao case, wity the reasoning that Julie was an OPA member and that they should handle it. He presents his findings to Captain Shaddid and she tells him to drop the case, too.

Miller has become obsessed with Julie, however, and keeps digging. Captain Shaddid, in collusion with the OPA, fires Miller; she gave him the case only because she didn't think he would actually solve it. Miller's replacement partner, Octavia Muss, tells him he's the station's joke, sending him into a deep depression. Even so, he still won't let the Mao case go.

On Tycho, Fred wants the Roci crew's depositions, so he can act as a mediator between Earth and Mars. After a few days of R&R, Holden concludes that he's bored and wants to take work. He receives a job from Fred tracking down Lionel Polanski, an assumed name for an OPA operative, on Eros Station. Holden claims the Roci as salvage, but since the MCRN probably wouldn't buy that, Fred helps him disguise the ship as a gas hauler.

Before he was fired, Detective Miller requested the docking logs for ships that could have come from the Donnager, as Dawes had dropped that Holden was still alive, and since Holden was the one that first investigated Julie's ship, Miller wants to know how this all ties together. Miller narrows the entries down to the Rocinante and heads off to Eros, where it's about due to dock.

On Eros, Holden and his crew go to the hotel where Polanski checked in and are promptly ambushed by gun-wielding assailants. Miller shows up and save the day, then joins their party. In Polanski's room, they find Julie Mao, dead, covered in some sort of infectious-looking brown rapidly spreading bacteria and black tendrils. Miller finds a log on her phone detailing the stages of her sickness, and notes that radiation seems to accelerate growth. They find coordinates for an asteroid where the ship that destroyed the Scopuli is docked.

A radiation attack is declared and station security begins herding people into radiation shelters. Miller recognizes some of the security as criminals from Ceres wearing the missing riot gear and knows something is up. Holden tells his crew to head back to the Rocinante while he and Miller investigate. They find that everyone in the radiation shelters has been gassed and dosed with a lethal amount of radiation, after which they get irradiated as well. On the way back to the Roci, riots break out between the crowds and the security, and Miller and Holden start bleeding from every orifice due to radiation sickness. The irradiated people have been infected with the same virus as Julie and start spilling out from the subway tubes.

Holden and Miller make it back to the Roci just in time; luckily, the advanced medical facilities flush the cancer from their bodies, though they are requested to take anti-cancer meds for the rest of their lives. While Naomi takes care of him, Holden confesses his love to her; she shoots him down because back on the Cant he fell in love with half the girls, and now he solely wants her because she's the only girl around.

Fred contacts Holden and sends along data from a chip that Lt. Kelly had on him, detailing that the EM signatures of the ships that destroyed the Donnager were made on Earth at the Bush Shipyards. Holden broadcasts this information publicly, causing Earth to preemptively attack Mars. Mars recalls its entire fleet from the Belt and forms a blockade against Earth.

The crew of the Roci, with Miller in tow, head to the asteroid Julie mentioned in her logs. There, they find the stealth ship that destroyed the Scopuli – the Anubis – deserted. The reactor is shut down and is covered in the flesh and body parts from the crews of both the stealth ship and the Scopuli. They find a video from the Protogen Corporation about the Phoebe bug, scientifically dubbed the "protomolecule"; Protogen had discovered that the Saturnian moon wasn't naturally formed, but was actually an alien weapon designed to attack Earth 2.3 billion years ago, when life was just forming, to reprogram humanity into something else. The whole war was simply a distraction, in order for Protogen to run their human experiments. The crew hoofs it before they get infected, but not before taking a souvenir safe; they nuke the stealth ship in their wake.

Holden and co. return to Tycho and tell Fred what they found. Realizing that Eros is beaming data to a hidden Protogen base, Miller contacts his old partner Havelock at Protogen security; Havelock says there's a secret base out there called Thoth and sends Miller the coordinates. Holden tells Miller that he is officially a member of the Roci crew. Miller is extremely happy to finally belong somewhere again that he subsequently weeps.

The Roci kicks off the attack on Thoth by taking out the two stealth ships docked there; then, Fred, Miller, and a group of OPA volunteers storm the station. They're met with only mild resistance; the security only has riot gear with plastic bullets. In the command center, they meet the head of Protogen bio research, Antony Dresden, who is very nonchalant about the whole thing. He explains that all the researchers there were turned into non-empathic psychopaths, and that Eros was simply a test to see what the protomolecule would do when introduced into human test subjects. Dresden explains how important this research is, since there is a clear alien threat trying to wipe out humanity. Before he can convince Holden and the others, Miller shoots him in the head. Holden is furious and kicks Miller out of his crew.

No one will hire Miller anywhere, so he begs Fred for a job; they come up with a plan to destroy Eros by flying the Nauvoo, a generational ship Fred was building for the Mormons, into it and crashing it into Sol.

Fred sends five ships full of fusion bombs to blow up Eros' docking ports, while the Rocinante acts as muscle to stop a UNN science vessel, accompanied by a corvette-class military ship, from docking. After the bomb ships are docked, Miller decides to remain on the station, so he can die when the bombs go off.

Fred launches the Nauvoo, but Eros manages to dodge the vessel. Eros blocks RADAR and LADAR, and begins accelerating towards Earth, faster than any ship can keep up with.

Holden contacts Miller to get the detonation codes for the fusion bombs, only to find he's still on the asteroid, which actually works out for the best: Miller hauls one of the bombs into the station on a cart, hoping to destroy the propelling capacities of protomolecule. Earth launches all of its nukes, targeting the transponders of the docked ships, because it cannot get a target lock any other way.

Miller, after listening closely to the voices coming from the communication system, realizes that it is actually Julie flying the station, while she is under the impression that she is driving her racing pinnace, the Razorback. Miller tells Holden to buy him some time, so Fred diverts the nukes off course, so they'll take longer to get there. Miller finds Julie, wakes her up, and convinces her to wrestle control away from the protomolecule. Julie successfully manages to divert the asteroid's trajectory away from Earth and crash it into Venus.

In the epilogue, Holden affirms that there are two kilometer-high crystal towers growing on the surface of Venus, implying that the protomolecule has survived.